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The different colors of branches represent the number of duplicated genes that trace back to that lineage of origin. Interpretation of a WGD is up to you. PUG is really trying to just show where duplications are. If there are a large number of duplicates combined with other evidence (like a Ks plot), then I am usually inclined to suspect a polyploid event. The SUMMARIZED_5080.txt file has the true counts based on the labeled nodes of the Labeled_Species_Tree.
The PUG looks like a great tool for studing WGD. However, i get 9 results files when I use demo data and a "New_File_Name.pdf"
after run "Rscript PUG_Figure_Maker.R PUG_Labeled_Species_Tree.tre PUG_SUMMARIZED_5080.txt New_File_Name.pdf", i don’t
know how to deduce WGD node ?So, could you give me some advises? Looking forward to your reply
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